Mon Oct 10 16:10:37 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 16:10:37 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3687 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5563891 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 7.612999 56.57200 ymin,ymax (A): -34.32200 29.66200 zmin,zma (A): -35.55600 25.78400 x,y,z range (A): 48.95900 63.98400 61.34000 scale (grids/A): 0.5563891 object centre (A): 32.09250 -2.330002 -4.886000 number of atom coordinates read : 3687 total number of charged atoms : 3583 net assigned charge : 5.200009 assigned positive charge : 549.3006 centred at (gu) : 89.36996 90.20181 91.24603 assigned negative charge : -544.1029 centred at (gu) : 89.30523 90.27158 91.30774 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7569 nv = 96 ne = 84 npr = 73850 no. pairs analyzed = 73850 no. exposed pairs = 4699 no. arc points = 32306 no. surface atoms = 1581 nbur = 2106 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 325 mr = 4038 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3800000 number of dielectric boundary points 3840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3284 ## 389 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9920 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0988023E-10 -3.3607575E-10 midg,1,midg; midg,igrid,midg 1.2598340E-09 -3.5514677E-10 1,midg,midg; igrid,midg,midg -3.2663014E-10 1.0853080E-09 gauss-seidel spectral radius is 0.9833966 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 16:10:38 rms-change max change #iterations 9.1394641E-02 15.63003 at 10iterations 6.5846136E-03 1.021427 at 20iterations 5.4269936E-04 6.7023277E-02 at 30iterations 8.1734994E-05 1.0026932E-02 at 40iterations 2.0113494E-05 2.5377274E-03 at 50iterations finished qdiffx linear iterations at : 16:10:40 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.0113494E-05 2.5377274E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 16:10:41 3.425u 0.160s 0:03.86 92.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 16:10:41 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3687 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.669167 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 7.612999 56.57200 ymin,ymax (A): -34.32200 29.66200 zmin,zma (A): -35.55600 25.78400 x,y,z range (A): 48.95900 63.98400 61.34000 scale (grids/A): 1.669167 object centre (A): 32.09250 -2.330002 -4.886000 number of atom coordinates read : 3687 total number of charged atoms : 3583 net assigned charge : 5.200009 assigned positive charge : 549.3006 centred at (gu) : 88.10871 90.60413 93.73695 assigned negative charge : -544.1029 centred at (gu) : 87.91522 90.81422 93.92265 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84111 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32306 grid for indexing accessible points = 1.400000 m= 27768 mr = 58519 m= 3176 mr = 19377 m= 93 mr = 1581 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 887 time to turn everything in is 0.5600000 number of dielectric boundary points 35665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 278 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 27627 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5563891 object centre at (A) : 32.09250 -2.330002 -4.886000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3813846E-03 1.2041585E-02 midg,1,midg; midg,igrid,midg 2.0042313E-02 1.5149749E-02 1,midg,midg; igrid,midg,midg 7.5324310E-04 -2.7113314E-05 gauss-seidel spectral radius is 0.9983475 estimated iterations to convergence 195 setup time was (sec) 0.8600000 now iterating at: 16:10:42 rms-change max change #iterations 3.917407 157.1896 at 10iterations 1.699893 72.10246 at 20iterations 0.7395427 24.83758 at 30iterations 0.3200496 10.05342 at 40iterations 0.1390894 4.339039 at 50iterations 6.0427688E-02 1.898178 at 60iterations 2.6293222E-02 0.8384743 at 70iterations 1.1450140E-02 0.3797994 at 80iterations 4.9849497E-03 0.1747231 at 90iterations 2.1758559E-03 7.6792240E-02 at 100iterations 9.5562940E-04 3.5821915E-02 at 110iterations 4.2228855E-04 1.2558937E-02 at 120iterations finished qdiffx linear iterations at : 16:10:48 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 4.2228855E-04 1.2558937E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 16:10:49 7.609u 0.226s 0:08.10 96.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 16:10:49 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3687 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.503751 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 7.612999 56.57200 ymin,ymax (A): -34.32200 29.66200 zmin,zma (A): -35.55600 25.78400 x,y,z range (A): 48.95900 63.98400 61.34000 scale (grids/A): 2.503751 object centre (A): 32.09250 -2.330002 -4.886000 number of atom coordinates read : 3687 total number of charged atoms : 3583 net assigned charge : 5.200009 assigned positive charge : 549.3006 centred at (gu) : 87.16287 90.90588 95.60519 assigned negative charge : -544.1029 centred at (gu) : 86.87266 91.22128 95.88390 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 195334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32306 grid for indexing accessible points = 1.400000 m= 94353 mr = 142839 m= 28681 mr = 75291 m= 5021 mr = 21772 m= 384 mr = 3349 m= 11 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 2977 time to turn everything in is 1.400000 number of dielectric boundary points 80395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 28640 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.669167 object centre at (A) : 32.09250 -2.330002 -4.886000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4406068E-02 0.4294490 midg,1,midg; midg,igrid,midg 0.2823824 0.3728950 1,midg,midg; igrid,midg,midg 3.1984322E-02 -2.5187902E-02 gauss-seidel spectral radius is 0.9992096 estimated iterations to convergence 281 setup time was (sec) 1.690000 now iterating at: 16:10:51 rms-change max change #iterations 10.09072 330.0276 at 10iterations 5.858821 149.2392 at 20iterations 3.388601 76.24080 at 30iterations 1.949267 42.28178 at 40iterations 1.120136 23.06690 at 50iterations 0.6399548 12.22466 at 60iterations 0.3659154 7.255581 at 70iterations 0.2081184 4.001553 at 80iterations 0.1182413 2.083738 at 90iterations 6.7197166E-02 1.172922 at 100iterations 3.8144976E-02 0.7065945 at 110iterations 2.1588175E-02 0.4674244 at 120iterations 1.2254135E-02 0.2225189 at 130iterations 6.9283131E-03 0.1193256 at 140iterations 3.9255624E-03 7.6234818E-02 at 150iterations 2.2215454E-03 4.3807983E-02 at 160iterations 1.2533524E-03 2.2924423E-02 at 170iterations 7.1083312E-04 1.1855125E-02 at 180iterations finished qdiffx linear iterations at : 16:11:02 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 7.1083312E-04 1.1855125E-02 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 16:11:02 12.593u 0.247s 0:13.11 97.8% 0+0k 0+0io 0pf+0w